Overview

We manually curated 500\(+\) multiple modality PPMI MRI subjects. 5 messages from this effort.

  1. Raw data quality is overall high
  1. Processing improves quality/usability further
  1. Detailed curation results provide a unique resource in itself
  1. Enables investigation of the “meaning” of M3RI at the individual level

  2. Empowers investigation of the “meaning” of M3RI at the population level

the PPMI500 cohort

Table 1. Baseline cohort for subjects with T1w IDPs and non-missing diagnosis.
CN GenAR LRRK2PD SporadicAR SporadicPD p
(N=47) (N=1) (N=4) (N=230) (N=217)
age 63.5 ± 12.5 71.9 ± NA 59.3 ± 7.1 67.7 ± 5.7 64.5 ± 9.4 < 0.001
Sex 0.026
    Female 23 (48.9%) 1 (100.0%) 3 (75.0%) 102 (44.3%) 72 (33.2%)
    Male 24 (51.1%) 0 ( 0.0%) 1 (25.0%) 128 (55.7%) 145 (66.8%)
duration.yrs         2.1 ± 0.7     1.0 ± 0.7 0.002
updrs.totscore 5.3 ± 3.8 14.0 ± NA 30.3 ± 13.1 12.1 ± 9.3 36.5 ± 15.0 < 0.001
CSFSAA < 0.001
    Negative 36 (85.7%) 1 (100.0%) 2 (50.0%) 82 (38.7%) 10 ( 4.9%)
    Positive 6 (14.3%) 0 ( 0.0%) 2 (50.0%) 130 (61.3%) 194 (95.1%)
LEDD 0.0 ± 0.0 0.0 ± NA 259.0 ± 317.7 1.3 ± 19.8 3.6 ± 30.3 < 0.001
hasDTI 0.117
    FALSE 9 (19.1%) 1 (100.0%) 1 (25.0%) 57 (24.8%) 38 (17.5%)
    TRUE 38 (80.9%) 0 ( 0.0%) 3 (75.0%) 173 (75.2%) 179 (82.5%)
hasfMRI 0.003
    FALSE 5 (10.6%) 1 (100.0%) 0 ( 0.0%) 12 ( 5.2%) 15 ( 6.9%)
    TRUE 42 (89.4%) 0 ( 0.0%) 4 (100.0%) 218 (94.8%) 202 (93.1%)

1. Data quality is overall high

How do we define M3RI quality?

  • we manually QC’d each modality for each of 500 baseline subjects

    • characterize reasons for failure

what is the QC protocol?

  • Review QC protocol – generally speaking

what are the QC results?

  • Summarize QC results for each modality

    • raw data QC and failure rates
  • Summarize results for “joint” quality - how many subjects are high quality across all modalities at once?

Tables of Manual QC results

Table 2 Patterns of QC results by modality: FLAIR
T2Flair p
(N=549)
qcfail_orientation
    True 1 (100.0%)
qcfail_intensity_saturation
    True 4 (100.0%)
qcfail_background_noise
    True 6 (100.0%)
qcfail_motion
    True 10 (100.0%)
qcfail_other
    True 2 (100.0%)
qchuman_FLAIR < 0.001
    False 25 ( 4.6%)
    True 524 (95.4%)
has_humanqc
    1 549 (100.0%)
Table 3 Patterns of QC results by modality: T1w
T1w p
(N=523)
qcfail_background_noise
    True 2 (100.0%)
qcfail_motion
    True 4 (100.0%)
qcfail_other
    True 4 (100.0%)
qchuman_T1w < 0.001
    False 10 ( 1.9%)
    True 513 (98.1%)
has_humanqc
    1 523 (100.0%)
Table 4 Patterns of QC results by modality: NM
Neuromelanin p
(N=502)
NM_QC_Ratings_Z < 0.001
    0 88 (18.3%)
    1 393 (81.7%)
NM_QC_Ratings_SNVol < 0.001
    0 7 ( 1.5%)
    1 474 (98.5%)
NM_QC_Ratings_AvgIntensity < 0.001
    0 5 ( 1.0%)
    1 473 (99.0%)
NM_QC_Ratings_SDIntensity < 0.001
    0 5 ( 1.0%)
    1 473 (99.0%)
NM_QC_Ratings_MaxIntensity < 0.001
    0 5 ( 1.0%)
    1 473 (99.0%)
NM_QC_Ratings_Failures < 0.001
    0 386 (80.8%)
    1 81 (16.9%)
    2 6 ( 1.3%)
    3 4 ( 0.8%)
    4 1 ( 0.2%)
Table 5 Patterns of QC results by modality: DTI
DTIb0 DTIdwi p
(N=1204) (N=1340)
qcfail_orientation
    True 16 (100.0%) 16 (100.0%)
qcfail_phantom
    True 6 (100.0%) 6 (100.0%)
qcfail_intensity_saturation
    True 0 ( 0.0%) 4 (100.0%)
qcfail_background_noise
    True 50 (100.0%) 54 (100.0%)
qcfail_motion
    True 54 (100.0%) 70 (100.0%)
qcfail_signal_dropout
    True 14 (100.0%) 22 (100.0%)
qcfail_other 1.000
    GHOSTING 10 (62.5%) 10 (62.5%)
    True 6 (37.5%) 6 (37.5%)
qchuman_DTI 0.481
    False 94 ( 7.8%) 116 ( 8.7%)
    True 1110 (92.2%) 1224 (91.3%)
has_humanqc
    1 1204 (100.0%) 1340 (100.0%)
Table 6 Patterns of QC results by modality: rsfMRI
rsfMRI rsfMRI_LR rsfMRI_RL p
(N=2969) (N=187) (N=854)
qcfail_orientation
    True 9 (100.0%) 1 (100.0%) 16 (100.0%)
qcfail_phantom
    True 14 (100.0%) 0 ( 0.0%) 0 ( 0.0%)
qcfail_spacing
    True 14 (100.0%) 0 ( 0.0%) 0 ( 0.0%)
qcfail_intensity_saturation
    True 20 (100.0%) 10 (100.0%) 32 (100.0%)
qcfail_motion
    True 581 (100.0%) 0 ( 0.0%) 0 ( 0.0%)
qcfail_signal_dropout
    True 165 (100.0%) 15 (100.0%) 48 (100.0%)
qcfail_temporal_noise
    True 1 (100.0%) 1 (100.0%) 8 (100.0%)
qcfail_insufficient_volumes
    True 12 (100.0%) 0 ( 0.0%) 0 ( 0.0%)
qcfail_FOV
    True 1 (100.0%) 0 ( 0.0%) 0 ( 0.0%)
qcfail_other < 0.001
    472 volumes, restart appended to initial scan? 0 ( 0.0%) 0 ( 0.0%) 8 (33.3%)
    axial slices look wrong way around? 0 ( 0.0%) 1 (50.0%) 8 (33.3%)
    strange artifacts in tsnr 0 ( 0.0%) 1 (50.0%) 8 (33.3%)
    True 1 (50.0%) 0 ( 0.0%) 0 ( 0.0%)
    wrap-around artifact 1 (50.0%) 0 ( 0.0%) 0 ( 0.0%)
qchuman_rsfMRI 0.002
    False 457 (15.4%) 19 (10.2%) 96 (11.2%)
    True 2512 (84.6%) 168 (89.8%) 758 (88.8%)
has_humanqc
    1 2969 (100.0%) 187 (100.0%) 854 (100.0%)

T1w results

T1w QC summary
modality Total Successes Failures Percent_Success Percent_Failure failcat
T1w 523 513 10 98.08795 1.9120459 qchuman_T1w
T1w 523 521 2 99.61759 0.3824092 qcfail_background_noise
T1w 523 519 4 99.23518 0.7648184 qcfail_motion
T1w 523 519 4 99.23518 0.7648184 qcfail_other

Flair results

FLAIR QC summary
modality Total Successes Failures Percent_Success Percent_Failure failcat
T2Flair 549 524 25 95.44627 4.5537341 qchuman_FLAIR
T2Flair 549 548 1 99.81785 0.1821494 qcfail_orientation
T2Flair 549 545 4 99.27140 0.7285974 qcfail_intensity_saturation
T2Flair 549 543 6 98.90710 1.0928962 qcfail_background_noise
T2Flair 549 539 10 98.17851 1.8214936 qcfail_motion
T2Flair 549 547 2 99.63570 0.3642987 qcfail_other

DT results

DTI QC summary
modality Total Successes Failures Percent_Success Percent_Failure failcat
DTIb0 1204 1110 94 92.19269 7.8073090 qchuman_DTI
DTIdwi 1340 1224 116 91.34328 8.6567164 qchuman_DTI
DTIb0 1204 1188 16 98.67110 1.3289037 qcfail_orientation
DTIdwi 1340 1324 16 98.80597 1.1940299 qcfail_orientation
DTIb0 1204 1198 6 99.50166 0.4983389 qcfail_phantom
DTIdwi 1340 1334 6 99.55224 0.4477612 qcfail_phantom
DTIb0 1204 1204 0 100.00000 0.0000000 qcfail_intensity_saturation
DTIdwi 1340 1336 4 99.70149 0.2985075 qcfail_intensity_saturation
DTIb0 1204 1154 50 95.84718 4.1528239 qcfail_background_noise
DTIdwi 1340 1286 54 95.97015 4.0298507 qcfail_background_noise
DTIb0 1204 1150 54 95.51495 4.4850498 qcfail_motion
DTIdwi 1340 1270 70 94.77612 5.2238806 qcfail_motion
DTIb0 1204 1190 14 98.83721 1.1627907 qcfail_signal_dropout
DTIdwi 1340 1318 22 98.35821 1.6417910 qcfail_signal_dropout
DTIb0 1204 1188 16 98.67110 1.3289037 qcfail_other
DTIdwi 1340 1324 16 98.80597 1.1940299 qcfail_other

rsfMRI results

rsfMRI QC summary
modality Total Successes Failures Percent_Success Percent_Failure failcat
rsfMRI 2969 2512 457 84.60761 15.3923880 qchuman_rsfMRI
rsfMRI_LR 187 168 19 89.83957 10.1604278 qchuman_rsfMRI
rsfMRI_RL 854 758 96 88.75878 11.2412178 qchuman_rsfMRI
rsfMRI 2969 2960 9 99.69687 0.3031324 qcfail_orientation
rsfMRI_LR 187 186 1 99.46524 0.5347594 qcfail_orientation
rsfMRI_RL 854 838 16 98.12646 1.8735363 qcfail_orientation
rsfMRI 2969 2955 14 99.52846 0.4715392 qcfail_phantom
rsfMRI_LR 187 187 0 100.00000 0.0000000 qcfail_phantom
rsfMRI_RL 854 854 0 100.00000 0.0000000 qcfail_phantom
rsfMRI 2969 2955 14 99.52846 0.4715392 qcfail_spacing
rsfMRI_LR 187 187 0 100.00000 0.0000000 qcfail_spacing
rsfMRI_RL 854 854 0 100.00000 0.0000000 qcfail_spacing
rsfMRI 2969 2949 20 99.32637 0.6736275 qcfail_intensity_saturation
rsfMRI_LR 187 177 10 94.65241 5.3475936 qcfail_intensity_saturation
rsfMRI_RL 854 822 32 96.25293 3.7470726 qcfail_intensity_saturation
rsfMRI 2969 2388 581 80.43112 19.5688784 qcfail_motion
rsfMRI_LR 187 187 0 100.00000 0.0000000 qcfail_motion
rsfMRI_RL 854 854 0 100.00000 0.0000000 qcfail_motion
rsfMRI 2969 2804 165 94.44257 5.5574267 qcfail_signal_dropout
rsfMRI_LR 187 172 15 91.97861 8.0213904 qcfail_signal_dropout
rsfMRI_RL 854 806 48 94.37939 5.6206089 qcfail_signal_dropout
rsfMRI 2969 2968 1 99.96632 0.0336814 qcfail_temporal_noise
rsfMRI_LR 187 186 1 99.46524 0.5347594 qcfail_temporal_noise
rsfMRI_RL 854 846 8 99.06323 0.9367681 qcfail_temporal_noise
rsfMRI 2969 2957 12 99.59582 0.4041765 qcfail_insufficient_volumes
rsfMRI_LR 187 187 0 100.00000 0.0000000 qcfail_insufficient_volumes
rsfMRI_RL 854 854 0 100.00000 0.0000000 qcfail_insufficient_volumes
rsfMRI 2969 2968 1 99.96632 0.0336814 qcfail_FOV
rsfMRI_LR 187 187 0 100.00000 0.0000000 qcfail_FOV
rsfMRI_RL 854 854 0 100.00000 0.0000000 qcfail_FOV

NM results

NM QC summary
NM.QC.cat Total Successes Failures Percent_Success Percent_Failure failcat
overall 478 386 92 80.75314 19.246862 NM_QC_Ratings_Failures
z.coord 478 391 87 81.79916 18.200837 NM_QC_Ratings_Z
sn.vol 478 471 7 98.53556 1.464435 NM_QC_Ratings_SNVol
avg.int 478 473 5 98.95397 1.046025 NM_QC_Ratings_AvgIntensity
sd.int 478 473 5 98.95397 1.046025 NM_QC_Ratings_SDIntensity
max.int 478 473 5 98.95397 1.046025 NM_QC_Ratings_MaxIntensity

do a check based on rsfmri motion – if the qc data “makes sense”

do a check based on DTI – if the qc data “makes sense”

do a check based on NM – if the qc data “makes sense”

do a check based on FLAIR – if the qc data “makes sense”

do a check based on T1w – if the qc data “makes sense”

2. Detailed curation results provide a unique resource in itself

for algorithm developers

  • we ourselves benefit from this (will show examples)

for scientists

  • to have confidence (or at least context regarding quality) in looking at automated IDPs derived from these data

3. Processing improves quality/usability further

effect of processing by modality

  • for each, summarize how processing improves the data

    • rsfMRI is “easy” to see - throw away motion corrupted data

    • developed methodology specific for PPMI that was informed by this process

    • automated QC for these modalities for future work

we provide scientists handles on this so that can be “strict” or “loose” in data selection

  • we document these parameters

4. Enables investigation of the “meaning” of M3RI at the individual level

5. Empowers investigation of the “meaning” of M3RI at the population level

simlr

## [1] "     <0> BUILD-V <0> BUILD-V <0> BUILD-V <0> BUILD-V <0>    "
## [1] "initialDataTerm: -0.372650010297621  <o> mixer: pca  <o> E:  cca"
## [1] "Iteration: 1 bestEv: -0.0327933507588981 bestIt: 1 CE: -0.0327933507588981"
## [1] "Iteration: 2 bestEv: -0.0630145184881478 bestIt: 2 CE: -0.0630145184881478"
## [1] "Iteration: 3 bestEv: -0.0968209008706581 bestIt: 3 CE: -0.0968209008706581"
## [1] "Iteration: 4 bestEv: -0.0968209008706581 bestIt: 3 CE: -0.0870532158412072"
## [1] "Iteration: 5 bestEv: -0.0968209008706581 bestIt: 3 CE: -0.0869174491918662"
## [1] "Iteration: 6 bestEv: -0.0968209008706581 bestIt: 3 CE: -0.092816820015101"
## [1] "Iteration: 7 bestEv: -0.120174060553191 bestIt: 7 CE: -0.120174060553191"
## [1] "Iteration: 8 bestEv: -0.120174060553191 bestIt: 7 CE: -0.120174060553191"
## [1] "Iteration: 9 bestEv: -0.12581493976007 bestIt: 9 CE: -0.12581493976007"
## [1] "Iteration: 10 bestEv: -0.128566404189215 bestIt: 10 CE: -0.128566404189215"
## [1] "Iteration: 11 bestEv: -0.129545856667216 bestIt: 11 CE: -0.129545856667216"
## [1] "Iteration: 12 bestEv: -0.13209953844886 bestIt: 12 CE: -0.13209953844886"
## [1] "Iteration: 13 bestEv: -0.136764239989398 bestIt: 13 CE: -0.136764239989398"
## [1] "Iteration: 14 bestEv: -0.136764239989398 bestIt: 13 CE: -0.0756392704157992"
## [1] "Iteration: 15 bestEv: -0.136764239989398 bestIt: 13 CE: -0.0801460646909918"
## [1] "Iteration: 16 bestEv: -0.136764239989398 bestIt: 13 CE: -0.0813127215892158"
## [1] "Iteration: 17 bestEv: -0.136764239989398 bestIt: 13 CE: -0.0813127215892158"
## [1] "Iteration: 18 bestEv: -0.136764239989398 bestIt: 13 CE: -0.136546894715855"
## [1] "Iteration: 19 bestEv: -0.139231177436898 bestIt: 19 CE: -0.139231177436898"
## [1] "Iteration: 20 bestEv: -0.147375833711929 bestIt: 20 CE: -0.147375833711929"
## [1] "Iteration: 21 bestEv: -0.147375833711929 bestIt: 20 CE: -0.140165912343255"
## [1] "Iteration: 22 bestEv: -0.147375833711929 bestIt: 20 CE: -0.140165912343255"
## [1] "Iteration: 23 bestEv: -0.147375833711929 bestIt: 20 CE: -0.140165912343255"
## [1] "Iteration: 24 bestEv: -0.147375833711929 bestIt: 20 CE: -0.140165912343255"
## [1] "Iteration: 25 bestEv: -0.147375833711929 bestIt: 20 CE: -0.142603300356657"
## [1] "Iteration: 26 bestEv: -0.147375833711929 bestIt: 20 CE: -0.142603300356657"
## [1] 0.0630929
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## [1] 0.03095999
## [1] "1 0.0400357755810751"
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## [1] 0.03919301
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## [1] 0.01436859
## [1] 0.01814266
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## [1] "1 0.0750359938885412"
## [1] 0.04493444
## [1] 0.1125809
## [1] 0.07546835
## [1] "1 0.0549330571836182"
## [1] 0.02603415
## [1] 0.05414639
## [1] 0.06647391
## [1] "1 0.118521595218043"
## [1] 0.04272542
## [1] 0.07975711
## [1] 0.04239525
## [1] "1 0.4452017304738"
## [1] 0.04304212
## [1] 0.05476584
## [1] 0.03708388
## [1] "1 0.00330776124436703"
## [1] 0.03181756
## [1] 0.03243388
## [1] 0.04640582
## [1] "1 0.948508253740791"
## [1] 0.06655578
## [1] 0.06839427
## [1] 0.01590732
## [1] "1 0.72330040215693"
## [1] 0.0154856
## [1] 0.02257197
## [1] 0.02519842
## [1] "1 0.071921885311281"
## [1] 0.01837715
## [1] 0.05024716
## [1] 0.04997093
## [1] "1 0.617639396084375"
## [1] 0.0605691
## [1] 0.116757
## [1] 0.07546761
## [1] "1 0.268881609018105"
## [1] 0.06633092
## [1] 0.08038766
## [1] 0.08946624
## [1] "1 0.0635555173143578"
## [1] 0.06078885
## [1] 0.07235237
## [1] 0.03320166
## [1] "1 0.0772495056408294"
## [1] 0.06277849
## [1] 0.06907499
## [1] 0.02451351
## [1] "1 0.652967102154168"
## [1] 0.03819196
## [1] 0.08308102
## [1] 0.05618294
## [1] "1 0.102773856216944"
## [1] 0.02484044
## [1] 0.07820951
## [1] 0.008306815
## [1] "1 0.0832899537153189"
## [1] 0.03610768
## [1] 0.06570733
## [1] 0.04691317
## [1] "1 0.051203573311852"
## [1] 0.04241024
## [1] 0.07551714
## [1] 0.02287316
## [1] "1 0.0126698285088394"
## [1] 0.03192555
## [1] 0.04344844
## [1] 0.03156755
## [1] "1 0.00956121475379167"
## [1] 0.02104856
## [1] 0.0649079
## [1] 0.0180208
## [1] "1 0.16148777507621"
## [1] 0.01960253
## [1] 0.04306293
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## [1] "1 0.0503950715107181"
## [1] 0.04204938
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## [1] 0.04065948
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## [1] "1 0.0199213036312554"
## [1] 0.03220299
## [1] 0.06735252
## [1] 0.04200663
## [1] "1 0.274081720575057"
## [1] 0.01462172
## [1] 0.03904959
## [1] 0.01407211
## [1] "1 0.0467825633887689"
## [1] 0.06881481
## [1] 0.08099738
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## [1] "1 0.122582259172455"
## [1] 0.02522416
## [1] 0.04433409
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## [1] "1 0.590313197992923"
## [1] 0.04195973
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## [1] 0.03639515
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## [1] 0.03828957
## [1] 0.0419498
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## [1] "1 0.0210430656699457"
## [1] 0.03973611
## [1] 0.06136413
## [1] 0.0256119
## [1] "1 0.249424783537397"
## [1] 0.04674051
## [1] 0.06373942
## [1] 0.01353346
## [1] "1 0.20309331060424"
## [1] 0.05356098
## [1] 0.09452549
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## [1] "1 0.56699252753519"
## [1] 0.02876336
## [1] 0.09104336
## [1] 0.02855228
## [1] "1 0.0442650152963898"
## [1] 0.04259282
## [1] 0.09626909
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## [1] "1 0.0254021432991888"
## [1] 0.03816867
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## [1] "1 0.0330042481634965"
## [1] 0.005864365
## [1] 0.03390455
## [1] 0.02994949
## [1] "1 0.0415025307632421"
## [1] 0.03045308
## [1] 0.0453398
## [1] 0.03063926
## [1] "1 0.0485317867560451"
## [1] 0.02098169
## [1] 0.04667136
## [1] 0.0205433
## [1] "1 0.221197703317231"
## [1] 0.02825009
## [1] 0.08395947
## [1] 0.0163654
## [1] "1 0.0331833196804612"
## [1] 0.06827637
## [1] 0.08456064
## [1] 0.06209281
## [1] "1 0.113786966265866"
## [1] 0.03580802
## [1] 0.07874386
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## [1] 0.05758521
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## [1] 0.06868643
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## [1] 0.05564
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## [1] 0.05502952
## [1] "1 0.587176282924374"
## [1] 0.04066368
## [1] 0.03527615
## [1] 0.03610686
## [1] "1 0.00132705617918233"
## [1] 0.05889093
## [1] 0.05160893
## [1] 0.06224246
## [1] "1 0.0670994235322177"
## [1] 0.02493003
## [1] 0.07788846
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## [1] "1 0.0242276829624712"
## [1] 0.02786918
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## [1] "1 0.087813684505013"
## [1] 0.03467518
## [1] 0.07589571
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## [1] "1 0.31586539187297"
## [1] 0.05978308
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## [1] 0.0309592
## [1] 0.04773233
## [1] 0.0354711
## [1] "1 0.0136265568514024"
## [1] 0.04713433
## [1] 0.05349283
## [1] 0.04030734
## [1] "1 0.559946659467991"
## [1] 0.06111391
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## [1] 0.02169783
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## [1] 0.05513028
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## [1] "1 0.141613043712074"
## [1] 0.04852659
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## [1] "1 0.387182361652895"
## [1] 0.05788892
## [1] 0.0843384
## [1] 0.0216129
## [1] "1 0.0374318376245641"
## [1] 0.03105342
## [1] 0.03727803
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## [1] 0.02512108
## [1] 0.07223662
## [1] 0.03961764
## [1] "1 0.0343678488559571"
## [1] 0.01854065
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## [1] 0.047196
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## [1] 0.05281333
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## [1] 0.03855365
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## [1] 0.04489314
## [1] "1 0.121290868638493"
## [1] 0.03392788
## [1] 0.06008074
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## [1] "1 0.00545932036091891"
## [1] 0.06208573
## [1] 0.0688373
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## [1] "1 0.699649464625945"
## [1] 0.009284302
## [1] 0.04557386
## [1] 0.01069078
## [1] "1 0.00652772077655523"
## [1] 0.02575567
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## [1] 0.03213179
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## [1] 0.04118437
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## [1] 0.0558201
## [1] 0.0521762
## [1] 0.028283
## [1] "1 0.356186558503165"
## [1] 0.0109955
## [1] 0.06303201
## [1] 0.02731521
## [1] "1 0.138329646229258"
## [1] 0.04120813
## [1] 0.0495756
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## [1] "1 0.0528586571631784"
## [1] 0.05082004
## [1] 0.07823377
## [1] 0.04619435
## [1] "1 0.0170658100592988"
## [1] 0.00858112
## [1] 0.004596902
## [1] 0.009437389
## [1] "1 0.100905524126079"
## [1] 0.05102408
## [1] 0.08837339
## [1] 0.0531868
## [1] "1 0.0171382945300328"
## [1] 0.03291919
## [1] 0.0553402
## [1] 0.02796184
## [1] "1 0.337177807747296"
## [1] 0.05459665
## [1] 0.03900464
## [1] 0.03572071
## [1] "1 0.153461346358315"
## [1] 0.04726743
## [1] 0.06830262
## [1] 0.03259438
## [1] "1 0.415804645433589"
## [1] 0.0177201
## [1] 0.06061726
## [1] 0.02973647
## [1] "1 0.16571572102884"
## [1] 0.04017365
## [1] 0.09883411
## [1] 0.04943956
## [1] "1 0.16844120146565"
## [1] 0.03433618
## [1] 0.07503754
## [1] 0.03671217
## [1] "1 0.404340637721021"
## [1] 0.0340711
## [1] 0.04898522
## [1] 0.04845004
## [1] "1 0.0736905253475063"
## [1] 0.03212837
## [1] 0.07287336
## [1] 0.06014556
## [1] "1 0.604708481761244"
## [1] 0.06430525
## [1] 0.07926983
## [1] 0.0247576
## [1] "1 0.144684532290054"
## [1] 0.04720213
## [1] 0.09778086
## [1] 0.04477515
## [1] "1 0.0822021566562165"
## [1] 0.01946235
## [1] 0.04567663
## [1] 0.05489625
## [1] "1 0.00977641272576385"
## [1] 0.04997235
## [1] 0.08113583
## [1] 0.04181768
## [1] "1 0.227776216761175"
## [1] 0.05166893
## [1] 0.06268007
## [1] 0.04021258
## [1] "1 0.050305054255458"
## [1] 0.04414744
## [1] 0.05509166
## [1] 0.01084672
## [1] "1 0.222739058256784"
## [1] 0.01237579
## [1] 0.005355435
## [1] 0.01219065
## [1] "1 0.1687876333614"
## [1] 0.03688722
## [1] 0.1335837
## [1] 0.02755578
## [1] "1 0.485784902815789"
## [1] 0.07897884
## [1] 0.03711085
## [1] 0.02465954
## [1] "1 0.0123230111060842"
## [1] 0.0448215
## [1] 0.07793249
## [1] 0.01497113
## [1] "1 0.00453776382408584"
## [1] 0.02108004
## [1] 0.07203351
## [1] 0.02664318
## [1] "1 0.360589701654667"
## [1] 0.03816867
## [1] 0.04962869
## [1] 0.03666615
## [1] "1 0.0330042481634965"
## [1] 0.06027731
## [1] 0.08355711
## [1] 0.05492718
## [1] "1 0.539366919625769"
## [1] 0.03788948
## [1] 0.02895126
## [1] 0.03721508
## [1] "1 0.00432227230294628"
## [1] 0.04841777
## [1] 0.03165477
## [1] 0.033069
## [1] "1 0.0746250184154798"
## [1] 0.0630172
## [1] 0.0517884
## [1] 0.05298815
## [1] "1 0.0829313235481923"
## [1] 0.03965592
## [1] 0.06163888
## [1] 0.03030191
## [1] "1 0.358820793829194"
## [1] 0.009545613
## [1] 0.07979472
## [1] 0.01954466
## [1] "1 0.0585191639721679"
## [1] 0.06868643
## [1] 0.06292221
## [1] 0.05070293
## [1] "1 0.0185477389632554"
## [1] 0.07132661
## [1] 0.07377478
## [1] 0.02631914
## [1] "1 0.527004824669165"
## [1] 0.03441058
## [1] 0.09505394
## [1] 0.01677284
## [1] "1 0.0488496378477023"
## [1] 0.01610217
## [1] 0.07306119
## [1] 0.02858364
## [1] "1 0.0157040997167592"
## [1] 0.06325705
## [1] 0.1084706
## [1] 0.04432835
## [1] "1 0.0194102902393112"
## [1] 0.04399229
## [1] 0.07010635
## [1] 0.03007796
## [1] "1 0.307944925682457"
## [1] 0.05415916
## [1] 0.04006834
## [1] 0.02738588
## [1] "1 0.105228511657066"
## [1] 0.04336709
## [1] 0.06706398
## [1] 0.03467856
## [1] "1 0.0278014286085451"
## [1] 0.04909176
## [1] 0.09420704
## [1] 0.02671771
## [1] "1 0.152552318255103"
## [1] 0.04756534
## [1] 0.05353695
## [1] 0.01422154
## [1] "1 0.0159567027794037"
## [1] 0.04715246
## [1] 0.05558576
## [1] 0.02785374
## [1] "1 0.0467562147285988"
## [1] 0.04532046
## [1] 0.1340682
## [1] 0.02261944
## [1] "1 0.0205892991899342"
## [1] 0.04184438
## [1] 0.02770159
## [1] 0.03000734
## [1] "1 0.254904107118623"
## [1] 0.02094793
## [1] 0.05395701
## [1] 0.02896039
## [1] "1 0.662727805310266"
## [1] 0.02677782
## [1] 0.04816317
## [1] 0.02323123
## [1] "1 0.0720307668928356"
## [1] 0.04428827
## [1] 0.04965497
## [1] 0.01669672
## [1] "1 0.0597032323785957"
## [1] 0.06593947
## [1] 0.08173966
## [1] 0.02927645
## [1] "1 0.0102231872300007"
## [1] 0.05834271
## [1] 0.08402735
## [1] 0.03180263
## [1] "1 0.107761533416821"
## [1] 0.03695462
## [1] 0.05395324
## [1] 0.03501445
## [1] "1 0.0284423480687222"
## [1] 0.02674508
## [1] 0.05297481
## [1] 0.04305638
## [1] "1 0.0152850993354577"
## [1] 0.06800031
## [1] 0.07924679
## [1] 0.0293476
## [1] "1 0.137354527720979"
## [1] 0.04909237
## [1] 0.03752832
## [1] 0.02931085
## [1] "1 0.0163764661782822"
## [1] 0.03837174
## [1] 0.09515757
## [1] 0.01964217
## [1] "1 0.16916548982543"
## [1] 0.03735237
## [1] 0.06716148
## [1] 0.03686288
## [1] "1 0.0123505264571607"
## [1] 0.05561619
## [1] 0.1035607
## [1] 0.0543239
## [1] "1 0.678139952645981"
## [1] 0.04208442
## [1] 0.05712025
## [1] 0.01417198
## [1] "1 0.83175904487243"
## [1] 0.08236342
## [1] 0.09283336
## [1] 0.03569142
## [1] "1 0.774343043103551"
## [1] 0.04271123
## [1] 0.06501948
## [1] 0.04764576
## [1] "1 0.118975711224574"
## [1] 0.05231901
## [1] 0.04154095
## [1] 0.0189346
## [1] "1 0.504226123155032"
## [1] 0.04351042
## [1] 0.07920088
## [1] 0.04696099
## [1] "1 0.0498942977024452"
## [1] 0.02987292
## [1] 0.05440064
## [1] 0.05568823
## [1] "1 0.0205641883157072"
## [1] 0.03518637
## [1] 0.06482327
## [1] 0.01457954
## [1] "1 0.31120838382253"
## [1] 0.03586346
## [1] 0.06525843
## [1] 0.04924828
## [1] "1 0.0848066713776339"
## [1] 0.05856011
## [1] 0.05774023
## [1] 0.04834239
## [1] "1 0.140705367548224"
## [1] 0.04093962
## [1] 0.1164789
## [1] 0.05582157
## [1] "1 0.00227655973751552"

SiMLR permutation summary
permstate anv pvalt1 pvalrs pvaldt
original 0.0000047 0.0011691 0.0079420 0.0003504
perm 0.0694300 0.0802097 0.2667030 0.0798390
perm 0.1072594 0.8680470 0.3132921 0.0222560
perm 0.0243461 0.1413078 0.5740906 0.0056556
perm 0.0063436 0.1798453 0.0449181 0.0167461
perm 0.0710965 0.1128826 0.9834749 0.0242626
perm 0.0240338 0.7456317 0.0665245 0.0125568
perm 0.0213913 0.2119596 0.3868857 0.0027174
perm 0.0803078 0.0382954 0.6368228 0.0916118
perm 0.1414967 0.2344531 0.5574916 0.0469212
perm 0.1050222 0.2381957 0.0667943 0.0745796
perm 0.1907766 0.4492391 0.3834974 0.0571751
perm 0.6243029 0.8945569 0.3675913 0.3459025
perm 0.0008337 0.0580824 0.1650137 0.0005346
perm 0.0643833 0.1016979 0.4763794 0.0315559
perm 0.1460269 0.6870602 0.0925345 0.1338071
perm 0.0106873 0.0443860 0.7994354 0.0035969
perm 0.7901966 0.4075784 0.8025325 0.4682103
perm 0.0207943 0.5688331 0.6109862 0.0022387
perm 0.0295521 0.4142411 0.0774829 0.0216190
perm 0.0006825 0.2971841 0.1911848 0.0001482
perm 0.0947598 0.5302543 0.2436291 0.0236403
perm 0.0223964 0.0634172 0.5029030 0.0094847
perm 0.0009147 0.0705353 0.1314502 0.0007966
perm 0.0249533 0.1737466 0.2916859 0.0069855
perm 0.1985562 0.8680367 0.6774136 0.0325414
perm 0.0146067 0.0710195 0.1551414 0.0233536
perm 0.0196025 0.9963803 0.2418433 0.0035880
perm 0.6652362 0.3755459 0.8568189 0.3702365
perm 0.8058407 0.5812390 0.8286369 0.3912588
perm 0.0749508 0.8351105 0.0900523 0.0392643
perm 0.0448685 0.4374698 0.1231911 0.0240846
perm 0.0152548 0.0929824 0.3275293 0.0043716
perm 0.7758435 0.4446225 0.9288389 0.4930635
perm 0.0974853 0.0960748 0.9238726 0.0456830
perm 0.0690886 0.1556651 0.0452718 0.2670161
perm 0.0099900 0.0439791 0.5721626 0.0068389
perm 0.5147746 0.6636876 0.3875821 0.2499281
perm 0.0255923 0.0438977 0.4616903 0.0243061
perm 0.0019469 0.0264891 0.3289980 0.0008280
perm 0.1257993 0.0943011 0.2675880 0.0837799
perm 0.0267451 0.1978715 0.8388439 0.0075719
perm 0.1605452 0.4487515 0.3234861 0.0607759
perm 0.0541901 0.3548631 0.4592467 0.0106347
perm 0.0587621 0.8426991 0.0957213 0.0259452
perm 0.0853013 0.1784287 0.6893937 0.0217681
perm 0.0055960 0.0930459 0.7845574 0.0008070
perm 0.0060211 0.1623494 0.1943731 0.0022386
perm 0.0913966 0.0551502 0.3636889 0.0991148
perm 0.3502226 0.3775817 0.5509221 0.1273804
perm 0.1083685 0.0953034 0.8018574 0.0684454
perm 0.8016149 0.4136429 0.7170129 0.7642400
perm 0.0043876 0.0384879 0.1571281 0.0032148
perm 0.0620506 0.6822488 0.5852356 0.0091929
perm 0.0929356 0.4696312 0.0529441 0.1507264
perm 0.0400358 0.1018730 0.5759020 0.0296177
perm 0.0724556 0.0862836 0.3388286 0.0255312
perm 0.4021281 0.4322164 0.7817934 0.1310847
perm 0.0569052 0.0540474 0.5177170 0.0407529
perm 0.0750360 0.8257215 0.2711839 0.0257086
perm 0.0549331 0.7217294 0.2921537 0.0127905
perm 0.1185216 0.2418733 0.2809390 0.0494120
perm 0.4452017 0.9142723 0.6120951 0.1194419
perm 0.0033078 0.1132300 0.5610602 0.0006265
perm 0.9485083 0.6890804 0.8912457 0.6391186
perm 0.7233004 0.9193576 0.5098847 0.3335210
perm 0.0719219 0.1500068 0.1576127 0.0674096
perm 0.6176394 0.1902574 0.8471342 0.9370318
perm 0.2688816 0.1490747 0.7415507 0.1871537
perm 0.0635555 0.7984197 0.8479511 0.0088242
perm 0.0772495 0.1216349 0.2260567 0.0770116
perm 0.6529671 0.2899924 0.8405496 0.4115109
perm 0.1027739 0.3605125 0.6181047 0.0164950
perm 0.0832900 0.0961793 0.2305333 0.0550834
perm 0.0512036 0.1351332 0.5282547 0.0126801
perm 0.0126698 0.0508589 0.9829042 0.0045834
perm 0.0095612 0.2416418 0.5863402 0.0011179
perm 0.1614878 0.2291609 0.6379811 0.0405266
perm 0.0503951 0.7148919 0.1093369 0.0206718
perm 0.1830104 0.2935424 0.9890428 0.0480269
perm 0.1741116 0.5026333 0.2962551 0.0875897
perm 0.0199213 0.0254064 0.5499397 0.0169188
perm 0.2740817 0.4565420 0.5806345 0.0688302
perm 0.0467826 0.1513901 0.2377942 0.0209253
perm 0.1225823 0.3535417 0.6136291 0.0382534
perm 0.5903132 0.1871730 0.7036283 0.7227901
perm 0.4771564 0.1285610 0.7862284 0.6632872
perm 0.0128222 0.0971413 0.6561062 0.0027370
perm 0.0210431 0.0960209 0.2726164 0.0109766
perm 0.2494248 0.6314261 0.1392429 0.1658396
perm 0.2030933 0.2016776 0.3892755 0.0951724
perm 0.5669925 0.9017372 0.4840948 0.2259073
perm 0.0442650 0.3834788 0.6761647 0.0061651
perm 0.0254021 0.1158664 0.1227671 0.0191241
perm 0.0330042 0.4537452 0.0814735 0.0292072
perm 0.0415025 0.0616540 0.3070899 0.0174161
perm 0.0485318 0.3644509 0.9941358 0.0065105
perm 0.2211977 0.2176258 0.2491716 0.1556025
perm 0.0331833 0.5037781 0.6604987 0.0049106
perm 0.1137870 0.4380586 0.3557650 0.0372716
perm 0.7176083 0.8634680 0.5513603 0.3816730
perm 0.1839883 0.2040618 0.5379042 0.0898527
perm 0.0463070 0.6087771 0.4922447 0.0069033
perm 0.1426950 0.1552440 0.1620237 0.1751514
perm 0.0185477 0.0836147 0.4272136 0.0105034
perm 0.5871763 0.8943092 0.5416989 0.1892451
perm 0.0013271 0.3020791 0.8494149 0.0000920
perm 0.0670994 0.0475736 0.9978720 0.0432202
perm 0.0242277 0.0291041 0.5129707 0.0125404
perm 0.0878137 0.1413292 0.6113380 0.0703612
perm 0.3158654 0.3058350 0.6868090 0.1166325
perm 0.3136576 0.2328416 0.9915143 0.1570859
perm 0.0136266 0.0582303 0.3098123 0.0096531
perm 0.5599467 0.3081697 0.8486026 0.3014523
perm 0.0557059 0.0293154 0.4986820 0.0868731
perm 0.1610302 0.1703099 0.4003211 0.0743655
perm 0.1416130 0.6775072 0.0209411 0.8856745
perm 0.3871824 0.1356557 0.4107656 0.9508726
perm 0.0374318 0.0214268 0.2416790 0.1116836
perm 0.0382186 0.0605358 0.8970215 0.0143635
perm 0.0343678 0.3350868 0.1625251 0.0175428
perm 0.0366601 0.0619787 0.4672351 0.0130751
perm 0.5561954 0.3095874 0.7271770 0.3232198
perm 0.1616133 0.1152372 0.8813898 0.0938115
perm 0.1923067 0.3504283 0.5276240 0.0547172
perm 0.7258652 0.5943323 0.3963854 0.4515286
perm 0.0595112 0.4495713 0.5696871 0.0079844
perm 0.1212909 0.4557049 0.8296672 0.0188269
perm 0.0054593 0.1796309 0.7062818 0.0005414
perm 0.6996495 0.6201654 0.3274373 0.5327888
perm 0.0065277 0.0627990 0.9455332 0.0010927
perm 0.1733944 0.1267778 0.1533224 0.3927794
perm 0.2518207 0.2694057 0.1324061 0.6773695
perm 0.1638721 0.0568458 0.9528489 0.1787965
perm 0.3561866 0.2153563 0.5857127 0.1960760
perm 0.1383296 0.1902167 0.8546937 0.0431959
perm 0.0528587 0.7289491 0.0770520 0.0518193
perm 0.0170658 0.3383117 0.0405216 0.0082595
perm 0.1009055 0.0896738 0.7441577 0.0332771
perm 0.0171383 0.0307829 0.3841242 0.0189550
perm 0.3371778 0.0902334 0.5264933 0.5428351
perm 0.1534613 0.6960775 0.5423815 0.0240024
perm 0.4158046 0.4257152 0.4716179 0.1704779
perm 0.1657157 0.1687814 0.8978533 0.0513860
perm 0.1684412 0.0979562 0.8377187 0.1560366
perm 0.4043406 0.8597943 0.0914698 0.9780985
perm 0.0736905 0.0836189 0.6333398 0.0237988
perm 0.6047085 0.3721159 0.9754145 0.3108546
perm 0.1446845 0.1439272 0.7528806 0.0702540
perm 0.0822022 0.2586044 0.6378371 0.0134438
perm 0.0097764 0.3144236 0.3216937 0.0017270
perm 0.2277762 0.3717628 0.2783915 0.0942077
perm 0.0503051 0.1145443 0.1845273 0.0245335
perm 0.2227391 0.0792579 0.2357078 0.6285385
perm 0.1687876 0.1467620 0.8206785 0.0544414
perm 0.4857849 0.3336680 0.3264938 0.3102242
perm 0.0123230 0.1604735 0.2419496 0.0067785
perm 0.0045378 0.1040823 0.0241557 0.0181515
perm 0.3605897 0.1477988 0.5553645 0.2611679
perm 0.0330042 0.4537452 0.0814735 0.0292072
perm 0.5393669 0.1832187 0.5696622 0.7826845
perm 0.0043223 0.0750257 0.2081106 0.0025184
perm 0.0746250 0.0246266 0.1072645 0.8401808
perm 0.0829313 0.5088470 0.2901157 0.0203564
perm 0.3588208 0.2545915 0.6736570 0.2056361
perm 0.0585192 0.0684210 0.4396406 0.0199962
perm 0.0185477 0.0836147 0.4272136 0.0105034
perm 0.5270048 0.4450949 0.7424349 0.2029845
perm 0.0488496 0.2995701 0.4118366 0.0122171
perm 0.0157041 0.8232076 0.5981375 0.0015439
perm 0.0194103 0.7081408 0.0438179 0.0107465
perm 0.3079449 0.2383637 0.9796426 0.1557321
perm 0.1052285 0.0934900 0.8609546 0.0443603
perm 0.0278014 0.0145153 0.7033555 0.0278191
perm 0.1525523 0.4403063 0.4325935 0.0339006
perm 0.0159567 0.1972291 0.4869382 0.0047655
perm 0.0467562 0.0667625 0.1584228 0.0580237
perm 0.0205893 0.0667067 0.8420439 0.0037786
perm 0.2549041 0.1976972 0.6932001 0.1738760
perm 0.6627278 0.8070727 0.8688831 0.2337125
perm 0.0720308 0.5917468 0.8213298 0.0107102
perm 0.0597032 0.0556809 0.7055130 0.0486853
perm 0.0102232 0.0347012 0.9613956 0.0039314
perm 0.1077615 0.5833151 0.7243364 0.0154177
perm 0.0284423 0.1281072 0.6674129 0.0087022
perm 0.0152851 0.1267394 0.1038448 0.0071859
perm 0.1373545 0.4431139 0.4776568 0.0433358
perm 0.0163765 0.0282572 0.2131662 0.0305710
perm 0.1691655 0.6417073 0.2249495 0.0559773
perm 0.0123505 0.0658297 0.1835070 0.0121501
perm 0.6781400 0.8451845 0.6806925 0.2457390
perm 0.8317590 0.8303224 0.3975545 0.7816628
perm 0.7743430 0.5959346 0.5265119 0.5092359
perm 0.1189757 0.1273301 0.5804916 0.0392976
perm 0.5042261 0.2928782 0.7599939 0.2445645
perm 0.0498943 0.0951265 0.0336678 0.2589517
perm 0.0205642 0.3440710 0.3760162 0.0047590
perm 0.3112084 0.1026529 0.6954546 0.2563652
perm 0.0848067 0.9943544 0.2818580 0.0249202
perm 0.1407054 0.3576636 0.4492610 0.0382356
perm 0.0022766 0.4589839 0.4750495 0.0002665
## Warning: Using `bins = 30` by default. Pick better value with the argument
## `bins`.